1 Notes

  • raw metrics from Cell Ranger (CR) count runs
  • CR 6.1.1 (Gencode 40, ensembl v106)

2 Samples table

  • include percentage of swapped counts from swappedDrops() with different min.frac values

3 Metrics table

  • compare some metrics from CR counts output stored in metrics_summary.csv of each sample

4 Cells: P vs V per donor

5 Metrics totals

6 Metrics averages

7 Metrics plots

8 Metrics comparison

8.1 Preparation

8.2 Type

8.3 Sex

8.4 Batch

8.5 APOE

9 scFlow

  • use cells called from Cell Ranger

10 SessionInfo

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.2.0 (2022-04-22)
##  os       macOS Big Sur/Monterey 10.16
##  system   x86_64, darwin17.0
##  ui       X11
##  language (EN)
##  collate  en_GB.UTF-8
##  ctype    en_GB.UTF-8
##  tz       Europe/London
##  date     2022-06-15
##  pandoc   2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package              * version  date (UTC) lib source
##  abind                  1.4-5    2016-07-21 [1] CRAN (R 4.2.0)
##  assertthat             0.2.1    2019-03-21 [1] CRAN (R 4.2.0)
##  backports              1.4.1    2021-12-13 [1] CRAN (R 4.2.0)
##  beachmat               2.12.0   2022-04-26 [1] Bioconductor
##  beeswarm               0.4.0    2021-06-01 [1] CRAN (R 4.2.0)
##  Biobase              * 2.56.0   2022-04-26 [1] Bioconductor
##  BiocGenerics         * 0.42.0   2022-04-26 [1] Bioconductor
##  BiocNeighbors          1.14.0   2022-04-26 [1] Bioconductor
##  BiocParallel           1.30.3   2022-06-05 [1] Bioconductor
##  BiocSingular           1.12.0   2022-04-26 [1] Bioconductor
##  bitops                 1.0-7    2021-04-24 [1] CRAN (R 4.2.0)
##  brio                   1.1.3    2021-11-30 [1] CRAN (R 4.2.0)
##  broom                  0.8.0    2022-04-13 [1] CRAN (R 4.2.0)
##  bslib                  0.3.1    2021-10-06 [1] CRAN (R 4.2.0)
##  cachem                 1.0.6    2021-08-19 [1] CRAN (R 4.2.0)
##  callr                  3.7.0    2021-04-20 [1] CRAN (R 4.2.0)
##  car                    3.0-13   2022-05-02 [1] CRAN (R 4.2.0)
##  carData                3.0-5    2022-01-06 [1] CRAN (R 4.2.0)
##  cli                    3.3.0    2022-04-25 [1] CRAN (R 4.2.0)
##  codetools              0.2-18   2020-11-04 [1] CRAN (R 4.2.0)
##  colorspace             2.0-3    2022-02-21 [1] CRAN (R 4.2.0)
##  crayon                 1.5.1    2022-03-26 [1] CRAN (R 4.2.0)
##  crosstalk              1.2.0    2021-11-04 [1] CRAN (R 4.2.0)
##  data.table           * 1.14.2   2021-09-27 [1] CRAN (R 4.2.0)
##  DBI                    1.1.2    2021-12-20 [1] CRAN (R 4.2.0)
##  DelayedArray           0.22.0   2022-04-26 [1] Bioconductor
##  DelayedMatrixStats     1.18.0   2022-04-26 [1] Bioconductor
##  desc                   1.4.1    2022-03-06 [1] CRAN (R 4.2.0)
##  devtools               2.4.3    2021-11-30 [1] CRAN (R 4.2.0)
##  digest                 0.6.29   2021-12-01 [1] CRAN (R 4.2.0)
##  dplyr                  1.0.9    2022-04-28 [1] CRAN (R 4.2.0)
##  DT                   * 0.23     2022-05-10 [1] CRAN (R 4.2.0)
##  ellipsis               0.3.2    2021-04-29 [1] CRAN (R 4.2.0)
##  evaluate               0.15     2022-02-18 [1] CRAN (R 4.2.0)
##  fansi                  1.0.3    2022-03-24 [1] CRAN (R 4.2.0)
##  fastmap                1.1.0    2021-01-25 [1] CRAN (R 4.2.0)
##  fs                     1.5.2    2021-12-08 [1] CRAN (R 4.2.0)
##  generics               0.1.2    2022-01-31 [1] CRAN (R 4.2.0)
##  GenomeInfoDb         * 1.32.2   2022-05-15 [1] Bioconductor
##  GenomeInfoDbData       1.2.8    2022-05-06 [1] Bioconductor
##  GenomicRanges        * 1.48.0   2022-04-26 [1] Bioconductor
##  ggbeeswarm             0.6.0    2017-08-07 [1] CRAN (R 4.2.0)
##  ggplot2              * 3.3.6    2022-05-03 [1] CRAN (R 4.2.0)
##  ggpubr               * 0.4.0    2020-06-27 [1] CRAN (R 4.2.0)
##  ggrepel                0.9.1    2021-01-15 [1] CRAN (R 4.2.0)
##  ggsignif               0.6.3    2021-09-09 [1] CRAN (R 4.2.0)
##  glue                   1.6.2    2022-02-24 [1] CRAN (R 4.2.0)
##  gridExtra              2.3      2017-09-09 [1] CRAN (R 4.2.0)
##  gtable                 0.3.0    2019-03-25 [1] CRAN (R 4.2.0)
##  htmltools              0.5.2    2021-08-25 [1] CRAN (R 4.2.0)
##  htmlwidgets            1.5.4    2021-09-08 [1] CRAN (R 4.2.0)
##  IRanges              * 2.30.0   2022-04-26 [1] Bioconductor
##  irlba                  2.3.5    2021-12-06 [1] CRAN (R 4.2.0)
##  jquerylib              0.1.4    2021-04-26 [1] CRAN (R 4.2.0)
##  jsonlite               1.8.0    2022-02-22 [1] CRAN (R 4.2.0)
##  knitr                * 1.39     2022-04-26 [1] CRAN (R 4.2.0)
##  lattice                0.20-45  2021-09-22 [1] CRAN (R 4.2.0)
##  lifecycle              1.0.1    2021-09-24 [1] CRAN (R 4.2.0)
##  magrittr               2.0.3    2022-03-30 [1] CRAN (R 4.2.0)
##  Matrix                 1.4-1    2022-03-23 [1] CRAN (R 4.2.0)
##  MatrixGenerics       * 1.8.0    2022-04-26 [1] Bioconductor
##  matrixStats          * 0.62.0   2022-04-19 [1] CRAN (R 4.2.0)
##  memoise                2.0.1    2021-11-26 [1] CRAN (R 4.2.0)
##  munsell                0.5.0    2018-06-12 [1] CRAN (R 4.2.0)
##  pillar                 1.7.0    2022-02-01 [1] CRAN (R 4.2.0)
##  pkgbuild               1.3.1    2021-12-20 [1] CRAN (R 4.2.0)
##  pkgconfig              2.0.3    2019-09-22 [1] CRAN (R 4.2.0)
##  pkgload                1.2.4    2021-11-30 [1] CRAN (R 4.2.0)
##  prettyunits            1.1.1    2020-01-24 [1] CRAN (R 4.2.0)
##  processx               3.6.0    2022-06-10 [1] CRAN (R 4.2.0)
##  ps                     1.7.0    2022-04-23 [1] CRAN (R 4.2.0)
##  purrr                  0.3.4    2020-04-17 [1] CRAN (R 4.2.0)
##  R6                     2.5.1    2021-08-19 [1] CRAN (R 4.2.0)
##  Rcpp                   1.0.8.3  2022-03-17 [1] CRAN (R 4.2.0)
##  RCurl                  1.98-1.7 2022-06-09 [1] CRAN (R 4.2.0)
##  remotes                2.4.2    2021-11-30 [1] CRAN (R 4.2.0)
##  rlang                  1.0.2    2022-03-04 [1] CRAN (R 4.2.0)
##  rmarkdown              2.14     2022-04-25 [1] CRAN (R 4.2.0)
##  rprojroot              2.0.3    2022-04-02 [1] CRAN (R 4.2.0)
##  rstatix                0.7.0    2021-02-13 [1] CRAN (R 4.2.0)
##  rstudioapi             0.13     2020-11-12 [1] CRAN (R 4.2.0)
##  rsvd                   1.0.5    2021-04-16 [1] CRAN (R 4.2.0)
##  S4Vectors            * 0.34.0   2022-04-26 [1] Bioconductor
##  sass                   0.4.1    2022-03-23 [1] CRAN (R 4.2.0)
##  ScaledMatrix           1.4.0    2022-04-26 [1] Bioconductor
##  scales                 1.2.0    2022-04-13 [1] CRAN (R 4.2.0)
##  scater               * 1.24.0   2022-04-26 [1] Bioconductor
##  scuttle              * 1.6.2    2022-05-17 [1] Bioconductor
##  sessioninfo            1.2.2    2021-12-06 [1] CRAN (R 4.2.0)
##  SingleCellExperiment * 1.18.0   2022-04-26 [1] Bioconductor
##  sparseMatrixStats      1.8.0    2022-04-26 [1] Bioconductor
##  stringi                1.7.6    2021-11-29 [1] CRAN (R 4.2.0)
##  stringr                1.4.0    2019-02-10 [1] CRAN (R 4.2.0)
##  SummarizedExperiment * 1.26.1   2022-05-01 [1] Bioconductor
##  testthat               3.1.4    2022-04-26 [1] CRAN (R 4.2.0)
##  tibble                 3.1.7    2022-05-03 [1] CRAN (R 4.2.0)
##  tidyr                  1.2.0    2022-02-01 [1] CRAN (R 4.2.0)
##  tidyselect             1.1.2    2022-02-21 [1] CRAN (R 4.2.0)
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##  vctrs                  0.4.1    2022-04-13 [1] CRAN (R 4.2.0)
##  vipor                  0.4.5    2017-03-22 [1] CRAN (R 4.2.0)
##  viridis                0.6.2    2021-10-13 [1] CRAN (R 4.2.0)
##  viridisLite            0.4.0    2021-04-13 [1] CRAN (R 4.2.0)
##  withr                  2.5.0    2022-03-03 [1] CRAN (R 4.2.0)
##  xfun                   0.31     2022-05-10 [1] CRAN (R 4.2.0)
##  XVector                0.36.0   2022-04-26 [1] Bioconductor
##  yaml                   2.3.5    2022-02-21 [1] CRAN (R 4.2.0)
##  zlibbioc               1.42.0   2022-04-26 [1] Bioconductor
## 
##  [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
## 
## ──────────────────────────────────────────────────────────────────────────────